About Our Lab

Our research lab leads cutting-edge investigations in microbial genomics, transcriptomics, fungal pathogenesis, and the human microbiome. We focus on clinically significant pathogens like Candida spp. and mucormycosis-causing fungi, integrating wet lab (in vitro and in vivo) experimentation—including antifungal screening and nanoparticle synthesis, with robust in-house multi-omics data analysis.

We explore antimicrobial resistance, host-pathogen interactions, and microbial pathogenesis using advanced tools in molecular biology and bioinformatics. The lab features a high-performance Linux-based genome analysis workstation running pipelines for genomics, transcriptomics, and metagenomics.

Our team brings expertise in large-scale omics data analysis and visualization, using R and Python to decode complex biological systems and their relevance to human health. This includes investigations into immune-mediated disorders such as Kawasaki disease, where integrative multi-omics profiling provides comprehensive insights into disease pathophysiology and host immune responses.

Dr. Khem Raj

Dr. Khem Raj is an expert in microbial genomics, transcriptomics, and fungal pathogenesis. His research focuses on microbial-host interactions and antimicrobial resistance, combining experimental biology with integrative omics approaches. He specializes in data-driven insights using R and Python to explore complex host-pathogen dynamics. Under his leadership, the lab bridges molecular microbiology and computational biology to drive translational research on emerging pathogens.

Research Scholars

Preeti Negi

Preeti Negi

Research on green synthesis of silver nanoparticles using Trillium govanianum and their application in studying Candida auris pathogenesis. Combines principles of nanotechnology and computational docking to explore novel antifungal strategies.

Gurkeerat Kaur

Gurkeerat Kaur

Conducted research on the antifungal and antibiofilm activities of green-synthesized silver-graphene nanohybrids against multidrug-resistant Candida auris, encompassing synthesis, characterization, and comprehensive biological evaluations.

Milani Sharma

Milani Sharma

Focuses on microbial community profiling and genomics to investigate the diversity, composition, and functional roles of microbiomes in host-microbe interactions.

Kanika Multani

Kanika Multani

Genomic and transcriptomic analysis of mucormycosis using high-throughput sequencing and RNA-Seq workflows. Applies computational genomics to study fungal pathogens.

M.Sc. Students

Srishti Sharma

High-throughput sequencing data analysis of Mucormycosis, including RNA-Seq workflows and qPCR validation of immunological gene expression.

Ishika Saini

Currently engaged in genomic research on Candida auris, focusing on clade-wise differences, virulence factors, and antimicrobial resistance genes.

Collaborators

Dr. Manpreet Dhaliwal

Advanced Paediatric Centre
Postgraduate Institute of Medical Education and Research

Dr. Rakesh Yadav

Department of Medical Microbiology
Postgraduate Institute of Medical Education and Research

Research Projects

Ongoing Projects

  1. Whole Genome Sequencing of Mycobacterium leprae Clinical Strains for Determining Drug Resistance and Strain lineage in India: - A multicentre prospective study
    Role: Co-Investigator
    Funding Agency: ICMR
    Funding Amount: INR 2.9 Crore
  2. To discover novel genetic variants predisposing to Inborn Errors of Immunity in pediatric and adult mucormycosis patients
    Role: Co-Investigator
    Funding Agency: Indian Council of Medical Research (ICMR), New Delhi
    Funding Amount: INR 57.34 Lakhs

Completed Projects

  1. Deciphering the microbiome landscape of native and migrated ‘Pangwala’ tribal population of India
    Role: Principal Investigator
    Funding Agency: Department of Health Research, Govt. of India (File No. R.12020/13/2018-HR)
    Funding Amount: INR 28.26 lakhs
  2. A transcriptome-based study to evaluate the pathways associated with immune dysfunction in COVID-19 Associated Mucormycosis
    Role: Co-Investigator
    Funding Agency: Pfizer, Fungal Infections Study Forum (FISF)
    Funding Amount: INR 17 lakhs

Publications

  1. Vijeata, A., et al. (2025). Engineering fungicidal nitrogen-doped carbon dots from Trillium govanianum rhizomes: A theoretical and experimental approach against Candida auris. Applied Surface Science, 709:163789. DOI
  1. Sihag, S., et al. (2025). Antimicrobial and Anticancer Potential of Chitinophaga sp. S167 Mediated Synthesis of Silver Nanoparticles. ChemistrySelect, 10(21):e00768. DOI
  1. Dhaliwal, M., et al. (2024). Immune and metabolic perturbations in COVID‐19‐associated pulmonary mucormycosis: A transcriptome analysis of innate immune cells. Mycoses, 67(1), e13679. DOI
  1. Negi, P., et al. (2024). Antimicrobial and Antibiofilm Potential of Green-Synthesized Graphene–Silver Nanocomposite against Multidrug-Resistant Nosocomial Pathogens. Biomedicines, 12(5):1104. DOI
  1. Raj, K., et al. (2024). Decoding the role of oxidative stress resistance and alternative carbon substrate assimilation in the mature biofilm growth mode of Candida glabrata. BMC Microbiology, 24(1), 128. DOI
  1. Raj, K., et al. (2022). Possible Contribution of Alternative Transcript Isoforms in Mature Biofilm Growth Phase of Candida glabrata. Indian Journal of Microbiology, 62(4), 583-601. DOI
  1. Verma, N., et al. (2024). Anticandidal Efficacy of Green Synthesized Silver Nanoparticles Using Trans-Himalayan Plant Extracts Against Drug Resistant Clinical Isolates of Candida auris. Indian Journal of Microbiology, 64(4):1912-1928. DOI
  1. Patial, S., et al. (2024). Atherosclerosis: Progression, risk factors, diagnosis, treatment, probiotics and synbiotics as a new prophylactic hope. The Microbe, 5:100212. DOI
  1. Sharma, S., et al. (2023). Antimicrobial Studies on Garlic Lectin. Probiotics & Antimicrobial Proteins, 15(6):1501–1512. DOI
  1. Riyaz, M., Raj, K. (2023). Emerging Microbial Identification Technologies in the Era of OMICS and Genome Editing. In: Sobti RC, Kuhad RC, Lal R, Rishi P, eds. Role of Microbes in Sustainable Development: Human Health and Diseases. Springer Nature; pp. 37–63. DOI
  1. Kaur, U.J., et al. (2021). Potential of 1-(1-napthylmethyl)-piperazine, an efflux pump inhibitor against cadmium-induced multidrug resistance in Salmonella enterica serovar Typhi. Brazilian Journal of Microbiology, 52(3):1303–1313. DOI
  1. Sarkar, S., et al. (2017). Association of rheumatic fever & rheumatic heart disease with plausible early & late-stage disease markers. Indian Journal of Medical Research, 145(6):758. DOI
  1. Rishi, P., et al. (2020). Diet, Gut Microbiota and COVID-19. Indian Journal of Microbiology, 60(4):420–429. DOI

News and Events

Our lab presented research at the 15th National Biennial Conference of the Indian Society of Medical Mycologists, showcasing advancements in fungal disease diagnostics and therapeutics.

Graduate students secured the 2nd and 3rd prizes at the International Conference on Harnessing the Power of Microbes for Viksit Bharat, recognizing their innovative contributions to microbial research.

Lab members also presented their latest findings at the Computational Biology Conference 2025, highlighting the integration of bioinformatics tools in infectious disease studies.

Our lab has been awarded an ICMR research grant to advance investigations into mucormycosis, strengthening our efforts in combating this life-threatening fungal infection.

Join Us

Opportunities in microbiology, molecular biology and bioinformatics.

Email: khemrajthakur@gmail.com

Contact Us

Department of Microbiology
Basic Medical Sciences Block I, South Campus
Panjab University, Sector-25, Chandigarh-160014, India

Email: khemrajthakur@pu.ac.in
Mobile: +91 9876726053
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